## [1] "O77_p5_IFNg_R1_2.hicup.bam"

Truncation & Mapping

Truncation Frequency

Category Read 1 Read 2
Total 69,545,581 69,545,581
Not Truncated 40,427,228 40,342,336
Truncated 29,118,353 29,203,245

Truncated Read Length

Category Read 1 Read 2
Average Length Truncated 40 39.9

Mapping Efficiency

Category Read 1 Read 2
Too Short To Map 8,237,036 8,703,456
Unique Alignments 56,273,429 53,300,235
Multiple Alignments 2,096,046 2,824,716
Failed To Align 2,939,070 4,717,174
Paired 43,129,800 43,129,800

Truncation and Mapping Bar Plot

Filtering

Filtering Breakdown by Category

Category Count
Valid Pairs 16,280,045
Invalid Pairs 26,849,755
Same Circularised 210,844
Same Dangling Ends 3,449,351
Same Fragment Internal 12,977,003
Re Ligation 8,782,414
Contiguous Sequence 212,669
Wrong Size 1,217,474
Total Pairs 43,129,800

Filtering Breakdown Pie Chart

Ditag Length Distribution

Frequency Line Plot

Deduplication

Deduplication Summary Table

Category All Ditags Unique Ditags
Read Pairs 16,280,045 31,666
Cis-close (<10Kbp) 1,379,170 2,905
Cis-far (>10Kbp) 9,252,176 16,724
Trans 5,648,699 12,037

Deduplication Bar Chart

Analysis produced by HiCUP - a tool for mapping and performing quality control on Hi-C data

Babraham Bioinformatics